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Microbial Ecology Nov 2021Paediatric inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the digestive tract, comprising of Crohn's disease (CD), ulcerative colitis (UC), and,... (Review)
Review
Paediatric inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the digestive tract, comprising of Crohn's disease (CD), ulcerative colitis (UC), and, where classification is undetermined, inflammatory bowel disease unclassified (IBDU). Paediatric IBD incidence is increasing globally, with prevalence highest in the developed world. Though no specific causative agent has been identified for paediatric IBD, it is believed that a number of factors may contribute to the development of the disease, including genetics and the environment. Another potential component in the development of IBD is the microbiota in the digestive tract, particularly the gut. While the exact role that the microbiome plays in IBD is unclear, many studies acknowledge the complex relationship between the gut bacteria and pathogenesis of IBD. In this review, we look at the increasing number of studies investigating the role the microbiome and other biomes play in paediatric patients with IBD, particularly changes associated with IBD, varying disease states, and therapeutics. The paediatric IBD microbiome is significantly different to that of healthy children, with decreased diversity and differences in bacterial composition (such as a decrease in Firmicutes). Changes in the microbiome relating to various treatments of IBD and disease severity have also been observed in multiple studies. Changes in diversity and composition may also extend to other biomes in paediatric IBD, such as the virome and the mycobiome. Research into biome differences in IBD paediatric patients may help progress our understanding of the aetiology of the disease.
Topics: Child; Colitis, Ulcerative; Crohn Disease; Humans; Inflammatory Bowel Diseases; Microbiota; Mycobiome
PubMed: 33666710
DOI: 10.1007/s00248-021-01697-9 -
Scientific Reports Feb 2024Seborrheic dermatitis (SD) affects 2-5% of the global population, with imbalances in the skin microbiome implicated in its development. This study assessed the impact of...
Seborrheic dermatitis (SD) affects 2-5% of the global population, with imbalances in the skin microbiome implicated in its development. This study assessed the impact of an oily suspension containing Lactobacillus crispatus P17631 and Lacticaseibacillus paracasei I1688 (termed EUTOPLAC) on SD symptoms and the skin mycobiome-bacteriome modulation. 25 SD patients were treated with EUTOPLAC for a week. Symptom severity and skin mycobiome-bacteriome changes were measured at the start of the treatment (T0), after seven days (T8), and three weeks post-treatment (T28). Results indicated symptom improvement post-EUTOPLAC, with notable reductions in the Malassezia genus. Concurrently, bacterial shifts were observed, including a decrease in Staphylococcus and an increase in Lactobacillus and Lacticaseibacillus. Network analysis highlighted post-EUTOPLAC instability in fungal and bacterial interactions, with increased negative correlations between Malassezia and Lactobacillus and Lacticaseibacillus genera. The study suggests EUTOPLAC's potential as a targeted SD treatment, reducing symptoms and modulating the mycobiome-bacteriome composition.
Topics: Humans; Mycobiome; Dermatitis, Seborrheic; Skin; Microbiota; Bacteria; Malassezia; Probiotics
PubMed: 38302693
DOI: 10.1038/s41598-024-53016-0 -
Journal of Ovarian Research Oct 2022To characterize the gut bacteriome, mycobiome and serum metabolome profiles in polycystic ovary syndrome (PCOS) patients with normal/overweight individuals and evaluate...
To characterize the gut bacteriome, mycobiome and serum metabolome profiles in polycystic ovary syndrome (PCOS) patients with normal/overweight individuals and evaluate a potential microbiota-related diagnostic method development for PCOS, 16S rRNA and ITS2 gene sequencing using 88 fecal samples and 87 metabolome analysis from serum samples are conducted and PCOS classifiers based on multiomics markers are constructed. There are significant bacterial, fungal community and metabolite differences among PCOS patients and healthy volunteers with normal/overweight individuals. Healthy individuals with overweight/obesity display less abnormal metabolism than PCOS patients and uniquely higher abundance of the fungal genus Mortierella. Nine bacterial genera, 4 predicted pathways, 11 fungal genera and top 30 metabolites are screened out which distinguish PCOS from healthy controls, with AUCs of 0.84, 0.64, 0.85 and 1, respectively. The metabolite-derived model is more accurate than the microbe-based model in discriminating normal BMI PCOS (PCOS-LB) from normal BMI healthy (Healthy-LB), PCOS-HB from Healthy-HB. Featured bacteria, fungi, predicted pathways and serum metabolites display higher associations with free androgen index (FAI) in the cooccurrence network. In conclusion, our data reveal that hyperandrogenemia plays a central role in the dysbiosis of intestinal microecology and the change in metabolic status in patients with PCOS and that its effect exceeds the role of BMI. Healthy women with high BMI showed unique microbiota and metabolic features.The priority of predictive models in discriminating PCOS from healthy status in this study were serum metabolites, fungal taxa and bacterial taxa.
Topics: Humans; Female; Polycystic Ovary Syndrome; Mycobiome; Overweight; RNA, Ribosomal, 16S; Metabolome; Bacteria
PubMed: 36303234
DOI: 10.1186/s13048-022-01051-8 -
Nutrients Apr 2023While the human gut is home to a complex and diverse community of microbes, including bacteria and fungi, research on the gut microbiome has largely focused on bacteria,... (Randomized Controlled Trial)
Randomized Controlled Trial
While the human gut is home to a complex and diverse community of microbes, including bacteria and fungi, research on the gut microbiome has largely focused on bacteria, with relatively little attention given to the gut mycobiome. This study aims to investigate how diets with different dietary macronutrient distributions impact the gut mycobiome. We investigated gut mycobiome response to high-carbohydrate, low-fat (HC) and low-carbohydrate high-fat (LC) diet interventions based on a series of 72-day feeding-based n-of-1 clinical trials. A total of 30 participants were enrolled and underwent three sets of HC and LC dietary interventions in a randomized sequence. Each set lasted for 24 days with a 6-day washout period between dietary interventions. We collected and analyzed the fungal composition of 317 stool samples before and after each intervention period. To account for intra-individual variation across the three sets, we averaged the mycobiome data from the repeated sets for analysis. Of the 30 participants, 28 (aged 22-34 years) completed the entire intervention. Our results revealed a significant increase in gut fungal alpha diversity ( < 0.05) and significant changes in fungal composition (beta diversity, < 0.05) after the HC dietary intervention. Specifically, we observed the enrichment of five fungal genera (, , , , sp.; FDR < 0.052) and depletion of one fungal genus (; FDR = 0.03) after the HC intervention. After the LC dietary intervention, one fungal genus was enriched ( sp.; FDR = 0.003), and five fungal genera were depleted ( spp., , , and ; FDR < 0.1). This study provides novel evidence on how the gut mycobiome structure and composition change in response to the HC and LC dietary interventions and reveals diet-specific changes in the fungal genera.
Topics: Humans; Mycobiome; Nutrients; Diet, Fat-Restricted; Gastrointestinal Microbiome; Carbohydrates
PubMed: 37432284
DOI: 10.3390/nu15092152 -
BMC Medicine Oct 2023The gut mycobiome of patients with lung adenocarcinoma (LUAD) remains unexplored. This study aimed to characterize the gut mycobiome in patients with LUAD and evaluate...
BACKGROUND
The gut mycobiome of patients with lung adenocarcinoma (LUAD) remains unexplored. This study aimed to characterize the gut mycobiome in patients with LUAD and evaluate the potential of gut fungi as non-invasive biomarkers for early diagnosis.
METHODS
In total, 299 fecal samples from Beijing, Suzhou, and Hainan were collected prospectively. Using internal transcribed spacer 2 sequencing, we profiled the gut mycobiome. Five supervised machine learning algorithms were trained on fungal signatures to build an optimized prediction model for LUAD in a discovery cohort comprising 105 patients with LUAD and 61 healthy controls (HCs) from Beijing. Validation cohorts from Beijing, Suzhou, and Hainan comprising 44, 17, and 15 patients with LUAD and 26, 19, and 12 HCs, respectively, were used to evaluate efficacy.
RESULTS
Fungal biodiversity and richness increased in patients with LUAD. At the phylum level, the abundance of Ascomycota decreased, while that of Basidiomycota increased in patients with LUAD. Candida and Saccharomyces were the dominant genera, with a reduction in Candida and an increase in Saccharomyces, Aspergillus, and Apiotrichum in patients with LUAD. Nineteen operational taxonomic unit markers were selected, and excellent performance in predicting LUAD was achieved (area under the curve (AUC) = 0.9350) using a random forest model with outcomes superior to those of four other algorithms. The AUCs of the Beijing, Suzhou, and Hainan validation cohorts were 0.9538, 0.9628, and 0.8833, respectively.
CONCLUSIONS
For the first time, the gut fungal profiles of patients with LUAD were shown to represent potential non-invasive biomarkers for early-stage diagnosis.
Topics: Humans; Mycobiome; Cross-Sectional Studies; Fungi; Adenocarcinoma of Lung; Biomarkers; Lung Neoplasms; Early Diagnosis
PubMed: 37904139
DOI: 10.1186/s12916-023-03095-z -
Cells Apr 2022Bacteria, as well as eukaryotes, principally fungi, of the upper respiratory tract play key roles in the etiopathogenesis of respiratory diseases, whereas the potential... (Review)
Review
Bacteria, as well as eukaryotes, principally fungi, of the upper respiratory tract play key roles in the etiopathogenesis of respiratory diseases, whereas the potential role of archaea remains poorly understood. In this review, we discuss the contribution of all three domains of cellular life to human naso- and oropharyngeal microbiomes, i.e., bacterial microbiota, eukaryotes (mostly fungi), as well as the archaeome and their relation to respiratory and atopic disorders in infancy and adolescence. With this review, we aim to summarize state-of-the-art contributions to the field published in the last decade. In particular, we intend to build bridges between basic and clinical science.
Topics: Archaea; Asthma; Bacteria; Child; Eukaryota; Fungi; Humans; Microbiota; Mycobiome
PubMed: 35455967
DOI: 10.3390/cells11081287 -
Fungal Genetics and Biology : FG & B Aug 2019Novel culture independent technologies have further elucidated the composition of the human mycobiome, though the role of fungi in human health and disease remains... (Review)
Review
Novel culture independent technologies have further elucidated the composition of the human mycobiome, though the role of fungi in human health and disease remains largely unknown. Recent studies have suggested conflicting roles for fungi in the gastrointestinal tract, underscoring the complexity of the interactions between the mycobiome, its bacterial counterpart, and the host. One key example is the observation that fungal taxa are overrepresented in patients with Clostridioides difficile infection (CDI), suggesting a role for fungi in this disease. Recent studies in murine models have demonstrated the ability of the commensal fungus Candida albicans to alter the course of CDI, supporting the notion that fungi play a role in this infection. This review summarizes current data on fungi and CDI, and shows that views of the dysbiotic state that is central to the pathogenesis of CDI are incomplete without consideration of the mycobiome.
Topics: Animals; Clostridioides difficile; Clostridium Infections; Disease Models, Animal; Dysbiosis; Fungi; Gastrointestinal Tract; Humans; Mice; Microbial Interactions; Mycobiome; Symbiosis
PubMed: 30978391
DOI: 10.1016/j.fgb.2019.04.007 -
Microbiome Apr 2022Extensive work has been accomplished to characterize the intestinal bacterial community, known as the microbiota, and its association with host health and disease....
BACKGROUND
Extensive work has been accomplished to characterize the intestinal bacterial community, known as the microbiota, and its association with host health and disease. However, very little is known about the spatiotemporal development and the origin of a minor intestinal fungal community, known as the mycobiota, in humans and animals, particularly in avian species.
RESULTS
In this study, we comprehensively characterized the biogeography and succession of the gastrointestinal (GI) mycobiota of broiler chickens and further revealed the fungal sources that are responsible for initial and long-term establishment of the mycobiota in the GI tract. Using Illumina sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes, we detected significant spatial and temporal differences in the mycobiota along the GI tract. In contrary to the microbiota, the mycobiota was more diverse in the upper than the lower GI tract with no apparent trend of succession up to 42 days of age. The intestinal mycobiota was dominated by the phyla Ascomycota and Basidiomycota with Gibberella, Aspergillus, and Candida being the most abundant genera. Although the chicken mycobiota was highly dynamic, Fusarium pseudonygamai was dominant throughout the GI tract regardless of age in this study. The core chicken mycobiome consisted of 26 fungal taxa accounting for greater than 85% of the fungal population in each GI location. However, we observed high variations of the intestinal mycobiota among different studies. We also showed that the total fungal population varied greatly from 1.0 × 10 to 1.1 × 10 /g digesta along the GI tract and only accounted for less than 0.06% of the bacteria in day-42 broilers. Finally, we revealed that the mycobiota from the hatchery environment was responsible for initial colonization in the GI tract of newly hatched chickens, but was quickly replaced by the fungi in the diet within 3 days.
CONCLUSIONS
Relative to the intestinal microbiota that consists of trillions of bacteria in hundreds of different species and becomes relatively stabilized as animals age, the chicken intestinal mycobiota is a minor microbial community that is temporally dynamic with limited diversity and no obvious pattern of successive changes. However, similar to the microbiota, the chicken mycobiota is spatially different along the GI tract, although it is more diverse in the upper than the lower GI tract. Dietary fungi are the major source of the intestinal mycobiota in growing chickens. Video abstract.
Topics: Animals; Chickens; Fungi; Gastrointestinal Tract; Intestines; Mycobiome
PubMed: 35365230
DOI: 10.1186/s40168-022-01252-9 -
The New Phytologist Nov 2020That arbuscular mycorrhizal (AM) fungi covary with plant communities is clear, and many papers report nonrandom associations between symbiotic partners. However, these... (Review)
Review
That arbuscular mycorrhizal (AM) fungi covary with plant communities is clear, and many papers report nonrandom associations between symbiotic partners. However, these studies do not test the causal relationship, or 'codependency', whereby the composition of one guild affects the composition of the other. Here we outline underlying requirements for codependency, compare important drivers for both plant and AM fungal communities, and assess how host preference - a pre-requisite for codependency - changes across spatiotemporal scales and taxonomic resolution for both plants and AM fungi. We find few examples in the literature designed to test for codependency and those that do have been conducted within plots or mesocosms. Also, while plants and AM fungi respond similarly to coarse environmental filters, most variation remains unexplained, with host identity explaining less than 30% of the variation in AM fungal communities. These results combined question the likelihood of predictable co-occurrence, and therefore evolution of codependency, between plant and AM fungal taxa across locations. We argue that codependency is most likely to occur in homogeneous environments where specific plant - AM fungal pairings have functional consequences for the symbiosis. We end by outlining critical aspects to consider moving forward.
Topics: Codependency, Psychological; Mycobiome; Mycorrhizae; Plant Roots; Plants; Soil Microbiology; Symbiosis
PubMed: 32452032
DOI: 10.1111/nph.16676 -
American Journal of Veterinary Research Sep 2023To report the density, and constituents, of the mycobiome on the skin surface of normal dogs.
OBJECTIVE
To report the density, and constituents, of the mycobiome on the skin surface of normal dogs.
ANIMALS
20 normal dogs were recruited for this study, with informed consent in all cases.
METHODS
Flocked swabs were used to sample the skin surface and to sample the skin surface after superficial scraping with a blunted scapula. Both samples were taken within a brass guide with an internal area of 3.5 cm-2. Next-generation DNA sequencing was used to identify and quantify components of the mycobiome.
RESULTS
The median density of the mycobiome was 1.1 X 105 cm-2 (IQR, 27,561, 409,572). Cladosporium spp and Vishniacozyma victoriae were found on all 20 dogs.
CLINICAL RELEVANCE
Knowledge of the density and the composition of the cutaneous mycobiome will increase our understanding of skin biology and may have relevance to future therapeutic trials.
Topics: Dogs; Animals; Mycobiome; Skin; Fungi
PubMed: 37536686
DOI: 10.2460/ajvr.23.04.0071